Nextflow

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.title[
# Nextflow
]
.author[
### <b>Asma Ali</b> • 09-Dec-2023
]
.institute[
### Zifo RnD Solutions
]

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# Workflow

* Analysing data involves a sequence of tasks, including gathering, cleaning, and processing data.

* These sequence of tasks are called a workflow or a pipeline.

* These workflows typically require executing multiple software packages, sometimes running on different computing environments, such as a desktop or a compute cluster.

* Traditionally these workflows have been joined together in scripts using general purpose programming languages such as Bash or Python.

* However, as workflows become larger and more complex, the management of the programming logic and software becomes difficult.

]

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<div class="figure" style="text-align: center">
<img src="data:image/png;base64,#data/sarek-workflow.png" alt="Example bioinformatics variant calling workflow/pipeline diagram from nf-core." width="50%" />
<p class="caption">Example bioinformatics variant calling workflow/pipeline diagram from nf-core.</p>
</div>

]
  
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# Workflow Management Systems

* Workflow Management Systems (WfMS), such as Snakemake, Galaxy, and Nextflow have been developed specifically to manage computational data-analysis workflows in fields such as Bioinformatics, Imaging, Physics, and Chemistry.

* WfMS contain multiple features that simplify the development, monitoring, execution and sharing of pipelines.
 
 * Key features include;

* Run time management
    
    * Software management
    
    * Portability & Interoperability
    
    * Reproducibility
    
    * Resumability

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# Nextflow

<br>

<img src="data:image/png;base64,#data/nextflow-logo.png" width="50%" style="display: block; margin: auto;" />
  
<br>
<br>
  
 * Nextflow is a workflow orchestration engine and domain-specific language (DSL) that makes it easy to write data-intensive computational workflows.

* It is designed around the idea that the Linux platform is the lingua franca of data science. Linux provides many simple but powerful command-line and scripting tools that, when chained together, facilitate complex data manipulations.

* Nextflow extends this approach, adding the ability to define complex program interactions and a high-level parallel computational environment, based on the dataflow programming model.
 
 * Nextflow scripting is an extension of the Groovy programming language which, in turn, is a super-set of the Java programming language.
 
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presenter notes!

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# Nextflow Features

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* Nextflow’s core features are:

* Workflow portability so that it can be executed on multiple platforms
  
  * Reproducibility of configurations and versions
  
  * Scalability of parallelization and deployment

* Integration of existing tools, systems, and industry standards
  
  * Continuous checkpoints during pipleine execution to track intermediate outputs
  
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<div class="figure" style="text-align: center">
<img src="data:image/png;base64,#data/nextflow-features.png" alt="Some additional features of Nextflow." width="65%" />
<p class="caption">Some additional features of Nextflow.</p>
</div>
]

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# Setup

* Nextflow can be used on any POSIX-compatible system (Linux, macOS, Windows Subsystem for Linux, etc.).
 
 * Requirements

* Bash
    
    * Java 11 (or later, up to 18)
    
    * Git
    
    * Docker
    
 * Docker

* Ensure you have Docker running on your server.
    
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#Installation
    
Enter this command in your terminal to download nextflow:

```bash
wget -qO- https://get.nextflow.io | bash
```
Or, if you prefer curl:

```bash
curl -s https://get.nextflow.io | bash
```

Then ensure that the downloaded binary is executable:

```r
chmod +x nextflow
```

And put the nextflow executable into your ``$PATH``. The executable could be in ``/usr/local/bin``, ``/bin/``, etc.

To test that the environment is working correctly, type the following into the terminal:

```r
nextflow info
```

This should come up with the Nextflow version and runtime information:

```r
Version: 22.10.4 build 5836
Created: 09-12-2022 09:58 UTC
System: Linux 5.15.0-47-generic
Runtime: Groovy 3.0.13 on OpenJDK 64-Bit Server VM 17.0.3-internal+0-adhoc..src
Encoding: UTF-8 (UTF-8)
```

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# Thank you. Questions?

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<p class="smaller">
<span class="small" style="line-height: 1.2;">Graphics from </span><img src="./assets/freepik.jpg" style="max-height:20px; vertical-align:middle;"><br>
Created: 09-Dec-2023 • James Ashmore • <a href="https://www.zifornd.com/category/omics-bioinformatics">Bioinformatics</a> • <a href="https://www.zifornd.com">Zifo</a>
</p>
]